Initial cases of COVID-19 reported in Hong Kong were mostly imported from China. However, most cases reported in February 2020 were locally-acquired infections, indicating local community transmissions. We extracted the demographic, clinical and epidemiological data from 50 COVID-19 patients, who accounted for 53.8% of the cases in Hong Kong by February 2020. Whole-genome sequencing of the SARS-CoV-2 were conducted to determine the phylogenetic relatedness and transmission dynamics. Only three (6.0%) patients required ICU admission. Phylogenetic analysis identified six transmission clusters. All locally-acquired cases harboured a common mutation Orf3a G251V and were clustered in two subclades in global phylogeny of SARS-CoV-2. The estimated time to the most recent common ancestor of local COVID-2019 outbreak was December 24, 2019 with an evolutionary rate of 3.04×10 ⁻³ substitutions per site per year. The reproduction number value was 1.84. Social distancing and vigilant epidemiological control are crucial to the containment of COVID-19 transmission. Article summary lines: A combined epidemiological and phylogenetic analysis of early COVID-19 outbreak in Hong Kong revealed that a SARS-CoV-2 variant with ORF3a G251V mutation accounted for all locally acquired cases, and that asymptomatic carriers could be a huge public health risk for COVID-19 control.

Background: Neonatal sepsis is a major cause of infant mortality, and it accounts for a significant consumption of antimicrobials in paediatrics. This is the first comprehensive study on neonatal sepsis in Hong Kong. Methods: From 2014 to 2023, all neonates admitted to a single institution with culture-proven infections from the blood and/or cerebrospinal fluid were selected and reviewed retrospectively. The infecting organisms, their antibiotic nonsusceptibility pattern, and the concordance of empirical antimicrobial therapy with the microbiological profiles were described and were further compared between infants of normal/low birth weight (≥1.5 kg) and very low/extremely low birth weight (<1.5 kg), early-onset sepsis (<72 h), and late-onset sepsis (4–28 days), the first and the second 5-year periods (2014–2018 vs. 2019–2023). Results: After contaminants were excluded, there were 118 affected neonates with 125 organisms identified. Fifty-nine were male. Thirty-four were very low/extremely low birth weight infants, and twenty-eight infants had early-onset sepsis. Patient demographics and the microbiology findings did not differ between the first 5 years and the latter 5 years. However, the incidence of neonatal sepsis was significantly lower in the latter 5 years (3.23 vs. 1.61 per 1000 live births, p < 0.001), the period that coincided with the COVID-19 pandemic. Escherichia coli was the most common Gram-negative pathogen. Streptococcus agalactiae and Streptococcus bovis group infections were more common in early-onset sepsis, while coagulase-negative Staphylococcus and non-E. coli Gram-negative pathogens were more likely to occur in late-onset sepsis. In very low/extremely low birth weight infants, the rate of cefotaxime or ceftriaxone nonsusceptibility among Gram-negative isolates was higher (p = 0.01), and concordance of empirical antimicrobial therapy was lower (p = 0.006). Conclusions: Management of neonatal sepsis remains challenging, and there is a need for optimising antimicrobial therapy, especially in preterm patients. Antepartum screening with intrapartum antibiotic prophylaxis is effective in reducing the risk of early-onset sepsis associated with S. agalactiae, while stringent infection control measures are important for the prevention of late-onset sepsis.

Objective: This study aimed to characterize the changing landscape of circulating SARS-CoV-2 lineages in the local community of Hong Kong throughout 2022. We examined how adjustments to quarantine arrangements influenced the transmission pattern of Omicron variants in a city with relatively rigorous social distancing measures at that time. Methods: In 2022, a total of 4684 local SARS-CoV-2 genomes were sequenced using the Oxford Nanopore GridION sequencer. SARS-CoV-2 consensus genomes were generated by MAFFT, and the maximum likelihood phylogeny of these genomes was determined using IQ-TREE. The dynamic changes in lineages were depicted in a time tree created by Nextstrain. Statistical analysis was conducted to assess the correlation between changes in the number of lineages and adjustments to quarantine arrangements. Results: By the end of 2022, a total of 83 SARS-CoV-2 lineages were identified in the community. The increase in the number of new lineages was significantly associated with the relaxation of quarantine arrangements (One-way ANOVA, F(5, 47) = 18.233, p < 0.001)). Over time, Omicron BA.5 sub-lineages replaced BA.2.2 and became the predominant Omicron variants in Hong Kong. The influx of new lineages reshaped the dynamics of Omicron variants in the community without fluctuating the death rate and hospitalization rate (One-way ANOVA, F(5, 47) = 2.037, p = 0.091). Conclusion: This study revealed that even with an extended mandatory quarantine period for incoming travelers, it may not be feasible to completely prevent the introduction and subsequent community spread of highly contagious Omicron variants. Ongoing molecular surveillance of COVID-19 remains essential to monitor the emergence of new recombinant variants.

Objective: The study aimed to characterize the changing landscape of circulating SARS-CoV-2 lineages in the local community of Hong Kong throughout 2022. We examined how adjustments to quarantine arrangements influenced the transmission pattern of Omicron variants in a city with relatively rigorous social distancing measures at that time. Methods: In 2022, a total of 4,684 local SARS-CoV-2 genomes were sequenced using the Oxford Nanopore GridION sequencer. SARS-CoV-2 consensus genomes were generated by MAFFT, and the maximum likelihood phylogeny of these genomes were determined using IQ-TREE. The dynamic changes in lineages were depicted in a time tree created by Nextstrain. Statistical analysis was conducted to assess the correlation between changes in the number of lineages and adjustments to quarantine arrangements. Results: By the end of 2022, a total of 83 SARS-CoV-2 lineages were identified in the community. The increase in the number of new lineages was significantly associated with the relaxation of quarantine arrangements (One-way ANOVA, F(5,47)=18.233, p<0.001)). Over time, Omicron BA.5 sub-lineages replaced BA.2.2 and became the predominant Omicron variants in Hong Kong. The influx of new lineages reshaped the dynamics of Omicron variants in the community without fluctuating the death rate and hospitalization rate (One-way ANOVA, F(5,47)=2.037, p=0.091). Conclusion: The study revealed that even with an extended mandatory quarantine period for incoming travelers, it may not be feasible to completely prevent the introduction and subsequent community spread of highly contagious Omicron variants. Ongoing molecular surveillance of COVID-19 remains essential to monitor the emergence of new recombinant variants.

The emergence of carbapenem-resistant non-typhoidal Salmonella species (CR-NTS) has been observed in recent years, causing increasing challenges in the clinical management and control of Salmonella infections. However, CR-NTS had not been comprehensively studied in Hong Kong previously. We retrieved archived non-typhoidal Salmonella isolates demonstrating carbapenem resistance from five public hospitals in Hong Kong during January 2020–June 2025. The isolates were characterised by NG-TEST CARBA-5 and subjected to whole-genome sequencing (WGS) and phylogenetic analysis. Clinical information of CR-NTS cases was also reviewed. Fourteen CR-NTS isolates (0.3%, 14/4404) were identified during the study period. All 13 CR-NTS isolates (one isolate could not be recovered) were NDM (New Delhi metallo-β-lactamase)-positive, with the first case identified in March 2023. WGS revealed six Group B Salmonella monophasic variants of Salmonella enterica serovar Typhimurium ST34 harbouring the bla_NDM-5 gene. The most common plasmid replicon co-present among bla_NDM-5-positive isolates was IncHI2–IncHI2A (63.6%, 7/11). Among cases of CR-NTS in our study, self-limiting gastroenteritis was the most common presentation (84.6%, 11/13); none presented with invasive infections; travel history was present in 7.7% (1/13). Phylogenetic analysis showed the genotypic relatedness of the ST34 isolates identified in Hong Kong to those on the Chinese mainland, with the possibility of local CR-NTS acquisition via imported food sources. Our findings highlighted the importance of a One Health approach to the control of CR-NTS and the need for continuous antimicrobial resistance surveillance of Salmonella spp. in Hong Kong.